Searching for genes influencing a complex disease: the case of coeliac disease

Artificial Intelligence Analysis of Celiac Disease Using an Autoimmune Discovery Transcriptomic Panel Highlighted Pathogenic Genes including BTLA

Celiac disease is a common immune-related inflammatory disease of the small intestine caused by gluten in genetically predisposed individuals. This research is a proof-of-concept exercise focused on using Artificial Intelligence (AI) and an autoimmune discovery gene panel to predict and model celiac disease. Conventional bioinformatics, gene set enrichment analysis (GSEA), and several machine learning and neural network techniques were used on a publicly available dataset (GSE164883). Machine learning and deep learning included C5, logistic regression, Bayesian network, discriminant analysis, KNN algorithm, LSVM, random trees, SVM, Tree-AS, XGBoost linear, XGBoost tree, CHAID, Quest, C&R tree, random forest, and neural network (multilayer perceptron). As a result, the gene panel predicted celiac disease with high accuracy (95–100%). Several pathogenic genes were identified, some of the immune checkpoint and immuno-oncology pathways. They included CASP3, CD86, CTLA4, FASLG, GZMB, IFNG, IL15RA, ITGAX, LAG3, MMP3, MUC1, MYD88, PRDM1, RGS1, etc. Among them, B and T lymphocyte associated (BTLA, CD272) was highlighted and validated at the protein level by immunohistochemistry in an independent series of cases. Celiac disease was characterized by high BTLA, expressed by inflammatory cells of the lamina propria. In conclusion, artificial intelligence predicted celiac disease using an autoimmune discovery gene panel.

Celiac disease

PURPOSE OF REVIEW

Research in celiac disease is unraveling new findings at a high rate, and major advances seem to occur in all areas such as genetics, environmental factor, pathophysiology, and even prospective therapeutic implications.

RECENT FINDINGS

New insight is being gained into the interplay between genetic and environmental factors causing celiac disease. In addition to the known human leukocyte antigen haplotypes, genome-wide studies have now identified additional susceptibility loci and the majority of newly discovered risk regions harbor genes controlling immune pathways. The mechanism of translocation of gliadin peptides across the intestinal barrier has been the subject of much investigation, and there is now evidence that the toxic 33-mer peptide can also be translocated transcellularly. As for the paracellular route, this appears to be enhanced by gliadin's stimulation of zonulin release. The growing role of the innate immunity is being recognized and the increased expression of some Toll-like receptors appears to delineate a new inherent defect in this branch of innate immunity. Finally, new perspectives are opening in the treatment of celiac disease based on new detoxified grains, enzymatic degradation of gluten, and prevention of its crossing the mucosal barrier.

SUMMARY

The pace of new knowledge in this 'ancient' disease is very fast, and this review outlines the principal lines of such exciting developments.